Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/8e489ce0e35439bc/finalize.log

@@ -0,0 +1,71 @@
+2026-10-02T21:40:04+09:00 launch finalize MemAvailable 108 GiB
+{
+ "command": "CUDA_VISIBLE_DEVICES='' python tools/prepare_dataset.py --dataset liu2021 (cxg_corpus env, bounded systemd unit)",
+ "tool_sha256": "36384262b23cf6260eff645812911c1a44f791ca8e4182765d91f2aabb3ccaef",
+ "PREPARE.json_sha256": "1e5ca31545be24c8b4ed9207de498cbab15d01eb3c8d297749f8557e31f5c0e5",
+ "folds.csv_sha256": "1d8aa9a8af520e73d14386b2573655286e1f5282d0209e0a6c83d4ce33e3dc5f",
+ "fold_sizes": {
+  "0": {
+   "test": 11,
+   "train": 43,
+   "inner_val": 4,
+   "test_groups": {
+    "COVID": 8,
+    "HC": 3
+   },
+   "alpha_genes_estimated": 10928
+  },
+  "1": {
+   "test": 12,
+   "train": 41,
+   "inner_val": 5,
+   "test_groups": {
+    "COVID": 10,
+    "HC": 2
+   },
+   "alpha_genes_estimated": 10883
+  },
+  "2": {
+   "test": 13,
+   "train": 41,
+   "inner_val": 4,
+   "test_groups": {
+    "COVID": 11,
+    "HC": 2
+   },
+   "alpha_genes_estimated": 10888
+  },
+  "3": {
+   "test": 10,
+   "train": 45,
+   "inner_val": 3,
+   "test_groups": {
+    "COVID": 8,
+    "HC": 2
+   },
+   "alpha_genes_estimated": 10925
+  },
+  "4": {
+   "test": 12,
+   "train": 42,
+   "inner_val": 4,
+   "test_groups": {
+    "COVID": 10,
+    "HC": 2
+   },
+   "alpha_genes_estimated": 10915
+  }
+ },
+ "usable_rows": 58,
+ "rows_in_fold_minus1": [
+  "HGR0000078_T0",
+  "HGR0000078_T1",
+  "HGR0000079_T0",
+  "HGR0000079_T1",
+  "HGR0000083_T0",
+  "HGR0000093_T1",
+  "HGR0000110_T0"
+ ],
+ "donors_in_folds": 41,
+ "donors_split_across_folds": 0
+}

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/9fe250a4bbad6f75/findings.log

@@ -0,0 +1,475 @@
+2026-10-02T21:25:00+09:00 launch findings MemAvailable 106 GiB
+2026-10-02T21:36:03+09:00 launch findings MemAvailable 108 GiB
+{
+ "spot": [
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "TAGTTGGTCAGTGCAT-5_1",
+   "our_umis": 3613,
+   "our_genes_in_cxg_var": 1466,
+   "equal_on_shared_genes": true,
+   "cxg_umis": 3519.0,
+   "our_umis_on_cxg_genes": 3519
+  },
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "AGTTGGTGTGTAATGA-7_1",
+   "our_umis": 4158,
+   "our_genes_in_cxg_var": 1467,
+   "equal_on_shared_genes": false,
+   "cxg_umis": 4061.0,
+   "our_umis_on_cxg_genes": 4060
+  },
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "GACCAATAGGCGTACA-16_4",
+   "our_umis": 1806,
+   "our_genes_in_cxg_var": 898,
+   "equal_on_shared_genes": true,
+   "cxg_umis": 1776.0,
+   "our_umis_on_cxg_genes": 1776
+  },
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "CGTTAGAGTGGTCCGT-8_1",
+   "our_umis": 3314,
+   "our_genes_in_cxg_var": 1404,
+   "equal_on_shared_genes": true,
+   "cxg_umis": 3234.0,
+   "our_umis_on_cxg_genes": 3234
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "CCCATACAGGATCGCA-03_4",
+   "our_umis": 522,
+   "our_genes_in_cxg_var": 280,
+   "equal_on_shared_genes": true,
+   "cxg_umis": 521.0,
+   "our_umis_on_cxg_genes": 521
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "TGCGGGTCAGCTTAAC-03_2",
+   "our_umis": 4639,
+   "our_genes_in_cxg_var": 1483,
+   "equal_on_shared_genes": true,
+   "cxg_umis": 4546.0,
+   "our_umis_on_cxg_genes": 4546
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "ATTATCCGTGCAGACA-4_1",
+   "our_umis": 3743,
+   "our_genes_in_cxg_var": 1492,
+   "equal_on_shared_genes": false,
+   "cxg_umis": 3677.0,
+   "our_umis_on_cxg_genes": 3676
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "TTTGCGCGTGGGTATG-11_4",
+   "our_umis": 2327,
+   "our_genes_in_cxg_var": 932,
+   "equal_on_shared_genes": true,
+   "cxg_umis": 2292.0,
+   "our_umis_on_cxg_genes": 2292
+  }
+ ],
+ "cxg": {
+  "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad": {
+   "cells": 125117,
+   "genes": 30000,
+   "cells_in_author_object": 125117,
+   "of_which_sorted": 36246,
+   "of_which_hto_not_singlet": 15273,
+   "obs_has_sorted_or_hto_columns": false
+  },
+  "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad": {
+   "cells": 246964,
+   "genes": 30000,
+   "cells_in_author_object": 246964,
+   "of_which_sorted": 100742,
+   "of_which_hto_not_singlet": 27042,
+   "obs_has_sorted_or_hto_columns": false
+  }
+ },
+ "selection_tv": 0.23350874938883667,
+ "coverage": {
+  "bulk_canonical_measured": 19060,
+  "sc_canonical_measured": 18976,
+  "pair_valid": 18553,
+  "panel6k_bulk": 5753,
+  "panel6k_sc": 5806,
+  "panel6k_both": 5681,
+  "bulk_duplicate_target_groups_summed": 10,
+  "bulk_has_ribosomal_and_mito_genes": true,
+  "note": "Unlike Giroux, the author bulk table keeps ribosomal-protein and mitochondrial genes."
+ },
+ "depth": {
+  "assigned_reads_paired_columns": {
+   "min": 11314446.0,
+   "median": 18300389.0,
+   "max": 28220948.0
+  },
+  "by_table": {
+   "B1_bulkRNAseq_countmtx.csv": 13311038.0,
+   "B2_B3_bulkRNAseq_countmtx.csv": 19730193.0
+  }
+ },
+ "author": {
+  "object_cells": 411902,
+  "object_min_nFeature_RNA": 201,
+  "object_max_nFeature_RNA": 3991,
+  "object_min_nCount_RNA": 244.0,
+  "object_max_percent_mito": 29.982046678635598,
+  "selected_cells": 224919,
+  "selected_min_nFeature_RNA": 201,
+  "selected_min_nCount_RNA": 244.0,
+  "selected_max_percent_mito": 29.982046678635598,
+  "selected_failing_conservative_rule": {
+   "genes_lt_200": 0,
+   "umis_lt_500": 2374,
+   "mito_gt_20pct": 3932
+  },
+  "author_cluster_doublets_in_selected": {
+   "Dblt": 4802
+  },
+  "conclusion": "The author object is already filtered (every cell has >= 200 genes, author percent.mito is a fraction, max ~0.3); it still holds HTO doublets/negatives (all demuxlet singlets) and the sorted fractions. The ImMicro rule (>=200 genes, >=500 UMIs, <=20 % mito) is applied on top. Author cluster-level 'Dblt' cells are not an HTO call and are kept (counted here)."
+ }
+}
+2026-10-02T21:36:56+09:00 launch findings MemAvailable 111 GiB
+{
+ "spot": [
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "TAGTTGGTCAGTGCAT-5_1",
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+   "our_genes_in_cxg_var": 1466,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 3519.0,
+   "our_umis_on_cxg_genes": 3519
+  },
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "AGTTGGTGTGTAATGA-7_1",
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+   "our_genes_in_cxg_var": 1467,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [
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+     "cxg_id": "ENSG00000291237",
+     "cxg_feature_name": "SOD2",
+     "cxg_count": 1.0,
+     "our_count_same_symbol": 1
+    }
+   ],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 4061.0,
+   "our_umis_on_cxg_genes": 4060
+  },
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "GACCAATAGGCGTACA-16_4",
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+   "our_genes_in_cxg_var": 898,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 1776.0,
+   "our_umis_on_cxg_genes": 1776
+  },
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "CGTTAGAGTGGTCCGT-8_1",
+   "our_umis": 3314,
+   "our_genes_in_cxg_var": 1404,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 3234.0,
+   "our_umis_on_cxg_genes": 3234
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "CCCATACAGGATCGCA-03_4",
+   "our_umis": 522,
+   "our_genes_in_cxg_var": 280,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 521.0,
+   "our_umis_on_cxg_genes": 521
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "TGCGGGTCAGCTTAAC-03_2",
+   "our_umis": 4639,
+   "our_genes_in_cxg_var": 1483,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 4546.0,
+   "our_umis_on_cxg_genes": 4546
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "ATTATCCGTGCAGACA-4_1",
+   "our_umis": 3743,
+   "our_genes_in_cxg_var": 1492,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [
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+     "cxg_feature_name": "PAXX",
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+     "our_count_same_symbol": null
+    }
+   ],
+   "equal_after_symbol_match": false,
+   "cxg_umis": 3677.0,
+   "our_umis_on_cxg_genes": 3676
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "TTTGCGCGTGGGTATG-11_4",
+   "our_umis": 2327,
+   "our_genes_in_cxg_var": 932,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 2292.0,
+   "our_umis_on_cxg_genes": 2292
+  }
+ ],
+ "cxg": {
+  "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad": {
+   "cells": 125117,
+   "genes": 30000,
+   "cells_in_author_object": 125117,
+   "of_which_sorted": 36246,
+   "of_which_hto_not_singlet": 15273,
+   "obs_has_sorted_or_hto_columns": false
+  },
+  "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad": {
+   "cells": 246964,
+   "genes": 30000,
+   "cells_in_author_object": 246964,
+   "of_which_sorted": 100742,
+   "of_which_hto_not_singlet": 27042,
+   "obs_has_sorted_or_hto_columns": false
+  }
+ },
+ "selection_tv": 0.23350874938883667,
+ "coverage": {
+  "bulk_canonical_measured": 19060,
+  "sc_canonical_measured": 18976,
+  "pair_valid": 18553,
+  "panel6k_bulk": 5753,
+  "panel6k_sc": 5806,
+  "panel6k_both": 5681,
+  "bulk_duplicate_target_groups_summed": 10,
+  "bulk_has_ribosomal_and_mito_genes": true,
+  "note": "Unlike Giroux, the author bulk table keeps ribosomal-protein and mitochondrial genes."
+ },
+ "depth": {
+  "assigned_reads_paired_columns": {
+   "min": 11314446.0,
+   "median": 18300389.0,
+   "max": 28220948.0
+  },
+  "by_table": {
+   "B1_bulkRNAseq_countmtx.csv": 13311038.0,
+   "B2_B3_bulkRNAseq_countmtx.csv": 19730193.0
+  }
+ },
+ "author": {
+  "object_cells": 411902,
+  "object_min_nFeature_RNA": 201,
+  "object_max_nFeature_RNA": 3991,
+  "object_min_nCount_RNA": 244.0,
+  "object_max_percent_mito": 29.982046678635598,
+  "selected_cells": 224919,
+  "selected_min_nFeature_RNA": 201,
+  "selected_min_nCount_RNA": 244.0,
+  "selected_max_percent_mito": 29.982046678635598,
+  "selected_failing_conservative_rule": {
+   "genes_lt_200": 0,
+   "umis_lt_500": 2374,
+   "mito_gt_20pct": 3932
+  },
+  "author_cluster_doublets_in_selected": {
+   "Dblt": 4802
+  },
+  "conclusion": "The author object is already filtered (every cell has >= 200 genes, author percent.mito is a fraction, max ~0.3); it still holds HTO doublets/negatives (all demuxlet singlets) and the sorted fractions. The ImMicro rule (>=200 genes, >=500 UMIs, <=20 % mito) is applied on top. Author cluster-level 'Dblt' cells are not an HTO call and are kept (counted here)."
+ }
+}
+2026-10-02T21:40:01+09:00 launch findings MemAvailable 108 GiB
+{
+ "spot": [
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "TAGTTGGTCAGTGCAT-5_1",
+   "our_umis": 3613,
+   "our_genes_in_cxg_var": 1466,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 3519.0,
+   "our_umis_on_cxg_genes": 3519
+  },
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "AGTTGGTGTGTAATGA-7_1",
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+   "our_genes_in_cxg_var": 1467,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [
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+     "cxg_feature_name": "SOD2",
+     "cxg_count": 1.0,
+     "our_count_same_symbol": 1
+    }
+   ],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 4061.0,
+   "our_umis_on_cxg_genes": 4060
+  },
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "GACCAATAGGCGTACA-16_4",
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+   "our_genes_in_cxg_var": 898,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 1776.0,
+   "our_umis_on_cxg_genes": 1776
+  },
+  {
+   "file": "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad",
+   "cell": "CGTTAGAGTGGTCCGT-8_1",
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+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
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+   "our_umis_on_cxg_genes": 3234
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "CCCATACAGGATCGCA-03_4",
+   "our_umis": 522,
+   "our_genes_in_cxg_var": 280,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
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+   "our_umis_on_cxg_genes": 521
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "TGCGGGTCAGCTTAAC-03_2",
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+   "our_genes_in_cxg_var": 1483,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 4546.0,
+   "our_umis_on_cxg_genes": 4546
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "ATTATCCGTGCAGACA-4_1",
+   "our_umis": 3743,
+   "our_genes_in_cxg_var": 1492,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [
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+     "cxg_feature_name": "PAXX",
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+     "our_count_same_symbol": null
+    }
+   ],
+   "equal_after_symbol_match": false,
+   "cxg_umis": 3677.0,
+   "our_umis_on_cxg_genes": 3676
+  },
+  {
+   "file": "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad",
+   "cell": "TTTGCGCGTGGGTATG-11_4",
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+   "our_genes_in_cxg_var": 932,
+   "equal_on_shared_ids": true,
+   "cxg_ids_not_in_hg19_table": [],
+   "equal_after_symbol_match": true,
+   "cxg_umis": 2292.0,
+   "our_umis_on_cxg_genes": 2292
+  }
+ ],
+ "cxg": {
+  "73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad": {
+   "cells": 125117,
+   "genes": 30000,
+   "cells_in_author_object": 125117,
+   "of_which_sorted": 36246,
+   "of_which_hto_not_singlet": 15273,
+   "obs_has_sorted_or_hto_columns": false
+  },
+  "e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad": {
+   "cells": 246964,
+   "genes": 30000,
+   "cells_in_author_object": 246964,
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+   "of_which_hto_not_singlet": 27042,
+   "obs_has_sorted_or_hto_columns": false
+  }
+ },
+ "selection_tv": 0.23350874938883667,
+ "coverage": {
+  "bulk_canonical_measured": 19060,
+  "sc_canonical_measured": 18976,
+  "pair_valid": 18553,
+  "panel6k_bulk": 5753,
+  "panel6k_sc": 5806,
+  "panel6k_both": 5681,
+  "bulk_duplicate_target_groups_summed": 10,
+  "bulk_has_ribosomal_and_mito_genes": true,
+  "note": "Unlike Giroux, the author bulk table keeps ribosomal-protein and mitochondrial genes."
+ },
+ "depth": {
+  "assigned_reads_paired_columns": {
+   "min": 11314446.0,
+   "median": 18300389.0,
+   "max": 28220948.0
+  },
+  "by_table": {
+   "B1_bulkRNAseq_countmtx.csv": 13311038.0,
+   "B2_B3_bulkRNAseq_countmtx.csv": 19730193.0
+  }
+ },
+ "author": {
+  "object_cells": 411902,
+  "object_min_nFeature_RNA": 201,
+  "object_max_nFeature_RNA": 3991,
+  "object_min_nCount_RNA": 244.0,
+  "object_max_percent_mito": 29.982046678635598,
+  "selected_cells": 224919,
+  "selected_min_nFeature_RNA": 201,
+  "selected_min_nCount_RNA": 244.0,
+  "selected_max_percent_mito": 29.982046678635598,
+  "selected_failing_conservative_rule": {
+   "genes_lt_200": 0,
+   "umis_lt_500": 2374,
+   "mito_gt_20pct": 3932
+  },
+  "author_cluster_doublets_in_selected": {
+   "Dblt": 4802
+  },
+  "conclusion": "The author object is already filtered (every cell has >= 200 genes, author percent.mito is a fraction, max ~0.3); it still holds HTO doublets/negatives (all demuxlet singlets) and the sorted fractions. The ImMicro rule (>=200 genes, >=500 UMIs, <=20 % mito) is applied on top. Author cluster-level 'Dblt' cells are not an HTO call and are kept (counted here)."
+ }
+}

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/c3bc04bdba1ddef0/bulk.log

@@ -0,0 +1,2 @@
+2026-10-02T21:16:09+09:00 launch bulk MemAvailable 103 GiB
+{"t": "2026-10-02T12:16:14.559899+00:00", "stage": "bulk", "status": "organized_with_explicit_masks", "n_samples": 73, "raw_count_eligible": true, "canonical_coverage": 0.9484002587450864, "duplicate_target_groups_summed": 10}

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/ccfbe8c2c37b2f6a/fullcells.log

@@ -0,0 +1,67 @@
+2026-10-02T21:38:23+09:00 launch fullcells MemAvailable 109 GiB
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+B3_SHD1_HC: 6174 cells
+B3_SHD3_HC: 5175 cells
+B3_SHD5_HC: 6397 cells
+B3_SHD6_HC: 2487 cells
+{"dataset": "liu2021", "n_cells": 191544, "nnz": 288833735, "sha256": "f262d7f30c70009863fc710f44cc672271e1d845fb4c3e6fa6bf00fd0853af8c", "checks": {"panel_columns_equal_cells_panel6k": true, "row_sums_equal_pseudo_raw_sum": true}, "builder": "processing/liu2021_v1_20261002/code/liu2021_full_cells.py (build_full_cells.read_library, same checks, streamed; re-verified on the written file)"}